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<BODY><h1>Introduction to MarvinSpace GUI Usage</h1>
<P><A HREF="space-index.html">Table of Contents</A> 
</P>

<h2><A class="anchor" NAME="introduction">Introduction</a></h2>

<p>
MarvinSpace is a Java-based 3-dimensional molecular structure visualization
program. Its main purpose is to display macromolecules including
proteins, nucleic acids, and protein-ligand complexes. MarvinSpace
is an interactive program, which means that it does not merely display a
static image but it allows the user to manipulate the structure: look at it from
different aspects, various distances, look inside etc.<br>
MarvinSpace can also be used to display and manipulate small molecules,
particularly if high quality rendering is required.
</p>

<p>MarvinSpace is built on OpenGL, the industry standard 3D visualization
language to render high quality molecular scenes. Beside high image quality,
OpenGL also provides efficiency that allows real-time manipulation of
molecular structures. OpenGL supports hardware acceleration, that is, it can
fully exploit the capabilities of the particular graphics card being used. </p>


<h2><A class="anchor" NAME="marvinview-gui">MarvinSpace GUI Overview</A></h2>

<h3><A class="anchor" NAME="canvas">Canvas</A></h3>

<p>
The canvas (or scene) is the image area that displays the molecular structures
in 3D. This is also an area that accepts mouse input events, like mouse motion
and mouse button clicks. These events are processed by the canvas and it reacts
to them in a predefined manner (though the default behaviour can be
<a href="#controlstab">changed easily</a>).
</p>

<h4><a class="anchor" name="eventsandactions">Events and actions:</a></h4>

<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Event</b></Th>
            <Th width="10%"><B>Action</b></Th>
            <th WIDTH="60%">Description</th>
        </TR>
        <TR>
            <TD><B>Mouse movement + Left button</b></td>
            <TD><B>Rotate</b></td>
            <td>Rotates the content of the scene (or the current cell in multiple
                cell view mode)
                about the two axes in the plane of the screen. If, however, mouse
                is moved outside the rotation sphere
<!--
                is moved outside the <a href="rotationsphere">rotation sphere</a>
-->
                the scene is rotated around the third axis that is perpendicular
                to the screen.</td>
        </tr>
        <TR>
            <TD><B>Mouse movement + Left button + Shift key</b> or
            <B>Mouse movement + Right button</b> </td>
            <TD><B>Move</b></td>
            <td>Moves the scene left-right and up-down.</td>
        </tr>
        <TR>
            <TD><B>Mouse movement + Middle button</b></td>
            <TD><B>Zoom</b></td>
            <td>Move the scene closer to or further from the viewer, depending on the direction of mouse motion.</td>
        </tr>
        <TR>
            <TD><B>Mouse wheel</b></td>
            <TD><B>Clipping</b></td>
            <td>Gradually removes parts of the structures that are near
                to the viewer's eyes.</td>
        </tr>
        <TR>
            <TD><B>Middle button click</b></td>
            <TD><B>Center</b></td>
            <td>Defines origin of the scene. The new origin (look at point)
                is the point where the mouse pointer was pointing at the
                click event.</td>
        </tr>
    </table>
</center>


<h3><a class="anchor" name="menubar">Menu Bar</a></h3>

<p>The main menu bar is located at the top of the MarvinSpace window. It consists
of seven submenus: <B>File</B>, <B>Edit</B>, <B>Display</B>, <B>Show</B>, <b>Animation</b>
<B>Layout</B> and <B>Help</B>.</p>

<h4><a class="anchor" name="filemenu">File menu</a></h4>

<p>The main function provided in the <B>File</B> submenu is
loading molecular structure files. These can
either be small molecules or a macromolecules (that is, proteins, protein-ligand
complexes, RNA, DNA etc). <br>
The structure opened is displayed in the current <a href="#layoutmenu">cell</a>
(marked by a thin red frame) and
is registered in the <a href="#selectionPanel">selection panel</a> on the right
hand side of the MarvinSpace window.
</p>

<p>There are two alternative ways to load new structures in MarvinSpace.
<B>Open</b> removes all existing objects (after confirmation)
and loads new structures in either one or more cells depending on user selection.
<br>
In contrast to this, <B>Add</b> keeps all previously loaded
structures and adds new ones to the current cell.</p>
<p><b>Open from RCSB PDB</b> connects http://www.rcsb.org to load a pdb file given by its identifier.</p>
<img alt="Open from RCSB PDB Dialog" src="space-gui_files/rcsb.png"/>
<p><b>Open property file</b> is to map volumetric data on molecular surfaces.
Currently supported property file formats are Gaussian Cube (*.cube) and Charmm (*.phi80).</p>

<p><b>Save screen</b> saves the canvas as a PNG, BMP or JPG file. It does full screen
anti-aliasing before image saving. The size of the image will be the same as the size of
the canvas.</p>

<p><b>Export image</b> saves the canvas in arbitrary size in the above formats. There is
a limitation: export image does not work properly if:</p>
<ul>
    <li>smooth background is enabled</li>
    <li>there are multiple cells</li>
    <li>there are any labels drawn in 2d</li>
</ul>


<p><B>Exit</B> leaves the program.</p>

<h4><a class="anchor" name="editmenu">Edit menu</a></h4>

<p>Selected molecules can be copied or cut, and molecules can be pasted with the
<b>Copy</b>, <b>Cut</b> and <b>Paste</b> menus.</p>

<p>The <b>Open MarvinSketch</b> menu enables molecule constructing on the fly, for
changes made in the Sketcher are reflected immediately to MarvinSpace. Selected ligands
will instantly appear for editing in the opening MarvinSketch window.</p>

<h4><a class="anchor" name="displaymenu">Display menu</a></h4>

<p>Submenus and options in the display menu allow to change the drawing
style, the coloring scheme and further properties of components
displayed. Classes of components can have different settings, for instance the atom
colors of proteins and that of ligands can be set independently. <br>
However, there are global parameters too, like the fog effect and anti-aliasing, that affect all
visible components.
</P>

<p>Display settings are applied to all visible components of the corresponding
category, that is, if the draw type of ligands is changed to spacefill, then
all ligands are drawn this way, that is, with large atom spheres.</p>

<h5><a class="anchor" name="drawtypemenu"><B>Draw type</b> submenu</a></h5>

<p>Component type specific visualization mode can be selected in this submenu.
Eight further submenus are available: Ligand, MacroMolecule, Water, Ion, Pharmacophore point,
    Pharmacophore arrow, Surface and Secondary structure.
    Note, that MacroMolecule refers to proteins and nucleic acid polymers too.
Also note, that not all visualization modes are available for all kinds of components.</P>


<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Ligand Draw Type</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Wire</b></td>
            <td>Draws bonds only as thin lines. The wire mode is the
                fastest, use it for very large structures or when graphic
                hardware exhibits poor performance.<br>
                <!--Note, that MarvinSpace 1.0-alpha represents triple
                and normalized (delocalized, aromatic) bonds as single ones.--></td>
        </tr>
        <tr>
            <td><B>Ball</b></td>
            <td>Only atoms are displayed as small spheres.</td>
        </tr>
        <tr>
            <td><B>Stick</b></td>
            <td>Only bonds are displayed as sticks (ie. cylinders) with smooth
                caps and joints.</td>
        </tr>
        <tr>
            <td><B>Ball and wire</b></td>
            <td>The combination of the <B>Ball</b> and the
                <B>Wire</b> modes.</td>
        </tr>
        <tr>
            <td><B>Ball and stick</b></td>
            <td>The combination of the <B>Ball</b> and the
                <B>Stick</b> modes. This gives very nice
                representation of the molecular structure, though in the case of
                large structures (that is, over 15000 atoms) the graphic
                performance drops sharply on non-hardware accelerated
                graphics cards. Good cards can easily
<!--
                <a href="graphiccard">graphics cards</a>. Good cards can easily
-->
                cope with very large structures that contain over 50000 atoms.</td>
        </tr>
        <tr>
            <td><B>Spacefill</b></td>
            <td>This mode represents atoms only, each with a sphere. The size of the sphere
                is equal to the van der Waals radius of the corresponding atom.
                Van der Waals radii are built in and
<!--
                <a href="vdwradius">Van der Waals radii</a> are built in and
-->
                cannot yet be modified by the user.</td>
        </tr>
        <tr>
            <td><B>Hydrogens</b></td>
            <td>An option, independent from all above draw type (that is, it can
                be combined with all draw types available. When box is checked,
                hydrogen atoms as well as bonds connecting heavy atoms and hydrogens
                are drawn, too.<br>
                Note, that MarvinSpace 1.3 is not capable of generating
                hydrogens not described in input files in the case of
                macromolecules. However, small molecules (excluding ligands
                in complexes) are automatically "hydrogenized". </td>
        </tr>
    </table>
</center>

<p>Note, that <B>Ligand</b> draw type is applied to all small
molecules, not only to ligands of protein-ligand complexes.</p>

<p>The next submenu, <B>MacroMolecule</b>, offers the same modes as ligand drawing.</p>

<!--
<p><B>Labels on selection</b> is a temporary implementation
of displaying atom labels. If this box is checked the residue atom
label of the selected atoms are displayed next to the atom. The residue atom
label consists of the residue name (3 letter abbreviation in the case of amino
acids, or 1 letter code in the case of nucleic acids), the residue sequence number,
the chain identifier and the atom label.<br>
Note, that further labels will also be available and alternative ways to display
label will also be implemented in next versions of MarvinSpace.
</p>
-->
<p>The next submenu, <B>Water</b> allows to specify the
representation of water molecules defined in PDB files.
The same modes are available as in case of ligand drawing.</P>

<p><B>Ion</b> sets the display mode of ions defined in PDB files, the
same options are available as for water molecules plus dotted mode, though the default draw
type is <B>Spacefill</b>.</p>

<p>The <B>Pharmacophore point</b> and <B>Pharmacophore arrow</b> submenus offers the display modes
<B>Solid</b>, <B>Wire</b> and
<B>Transparent</b>. <b>Dotted</b> mode is available in <B>Pharmacophore point</b> menu only.
    Read more about Pharmacophore representation <a href="#pharmacophore">here</a>.</P>

<p>In the <B>Surface</b> submenu four draw types are available:
<B>Dot</b>, <B>Mesh</b>, <B>Solid</b> and <b>Transparent</b>.</p>

<p>The next submenu is <B>Secondary structure</b>.</p>
    <blockquote>
    <b>Trace</b> is a connection of C alpha atoms with cylinders.<br>
    <b>Tube</b> is a smooth cylindrical tube representation of the C alpha atoms.<br>
    <b>Pipe and Plank</b> means the displaying of helices as cylinders, the sheets as boxes,
    and the others as tube.<br>
    The followings are slightly different versions of the standard secondary structure representation.<br>
    <b>Ribbon lines</b> is drawing as several "parallel", or offset curves,<br>
    <b>Ribbon</b> is a flat, polygonal representation,<br>
    <b>Cartoon square</b> is like a thick ribbon,<br>
    <b>Cartoon</b> is the common cartoon representation of secondary structures.
    </blockquote>


<p>The last submenu in <B>Draw type</b> is <b>Label</b>.</p>
    <blockquote>
    There are two types of labels available:<br>
    Labels can be <b>drawn in plane</b>, so that they won't be affected by depth cueing and clipping, their
    size will not change by zooming, and they will not be obscured by objects in the space.<br>
    Labels can also be rendered in 3D in exact depth.<br>
    The size of the labels can be chosen as Small, Medium or Large.<br>
    Border and Background drawing of labels can be enabled or disabled.
    </blockquote>



<h5><a class="anchor" name="colortypemenu"><B>Color type</b> submenu</a></h5>

<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Ligand</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Constant</b></td>
            <td>Depending on draw type atoms and bonds or all are painted the
                same color which by default is gold.</td>
        </tr>
        <TR>
            <TD><B>CPK</b></td>
            <td>Atoms are colored according to the <!--<a href="cpkcolors">-->CPK
                coloring schema<!--</a>--> in which the atom color depends on the
                atom type. <br>
                If bonds are also displayed then these
                are colored as the two atoms that they connect.<br>
                Note, that the colors of the most frequent atoms can be changed in the
                <a href=#options>Options dialog</a>.
            </td>
        </tr>
    </table>
</center>

<br>
<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>MacroMolecule</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Constant</b></td>
            <td>Depending on draw type atoms and bonds or all are painted gray.</td>
        </tr>
        <TR>
            <TD><B>CPK</b></td>
            <td>Atoms are colored according to the <!--<a href="cpkcolors">-->CPK
                coloring schema<!--</a>--> in which the atom color depends on the
                atom type. <br>
                Bonds displayed
                are colored by the colors of the two atoms that they connect.<br>
                Note, that the colors of the most frequent atoms can be changed in the
                <a href=#options>Options dialog</a>.</td>
        </tr>
        <tr>
            <td><B>Residue</b></td>
            <td>Atoms and bonds are colored according to the residue (amino acid
                or nucleic acid) type. <br>
                Note, that the colors schema can be changed in the
                <a href=#options>Options dialog</a>.
            </td>
        </tr>
        <tr>
            <td><B>Chain</b></td>
            <td>Atoms and bonds that are in the same chain (in a protein or in
                a nucleic acid) are colored the same, while different chains are
                colored by different colors.</td>
        </tr>
        <tr>
            <td><B>Secondary structure</b></td>
            <td>Atoms and bonds are colored according to the secondary structure
                type.</td>
        </tr>
        <tr>
            <td><B>Rainbow</b></td>
            <td>That is coloring by the increasing index of the carbon alpha atoms.</td>
        </tr>
        <tr>
            <td><B>B-factor</b></td>
            <td>Means coloring by the temperature factor, where colors are coming
            from a blue to yellow color palette.</td>
        </tr>
    </table>
</center>

<p><b>Water</b> molecules and <b>Ions</b> can be colored by constant or by CPK colors. </p>
<p>In case of <b>surfaces</b> the types introduced for macromolecules are available, and an
eighth option can also be selected: <B>Electrostatic potential</b>
that calculates electrostatic potential value for surface points and colors the
surface according to the current value at a given surface point.
By default negative potential is colored by blue while positive potential values are represented by
red. The intensity of colors varies according to the absolute value of the
electrostatic potential.
The color palette can be changed for example to rainbow and blue to green colors.
The coloring can <a href="#dynamicsurfacecolor">dynamically be adjusted</a>
independently for negative and for positive values.</p>

<p>The <b>Secondary Structures</b> can be colored as MacroMolecules except the CPK coloring.</p>



<!--
<a name="surfacemenu"></a><h4><B>Surface</b> submenu</h4>

<p>There are four types of molecular surfaces available in MarvinSpace: Connolly,
van der Waals, solvent accessible and blobby. Blobby molecule is yet experimental.</p>
-->

<h5><a class="anchor" name="qualitymenu"><B>Quality</b> submenu</a></h5>

<p>Three display qualities are provided by MarvinSpace: <B>High</b>,
<B>Medium</b> and <B>Low</b>.
Apparently, <B>High</b> gives the nicest and smoothest
representation, while <B>Low</b> enables the highest
performance, thus this is the most suitable for slow graphic cards. The rendering
quality is primarily determined by the number of triangles constituting atom
sphere and bond cylinders for structure display. In the case of surfaces the
resolution of a discrete grid in which the surface is approximated correlates with
 the rendering quality. The corresponding parameters are
wired in and cannot be changed by the user. Future version of MarvinSpace
will provide a dialog in the GUI to let the user tweak these parameters according
to needs and the performance of the graphic card.</p>

<p>Rendering quality autoscaling mechanism is also implemented, though in MarvinSpace 1.3
this is still experimental. Autoscaling decreases the current display quality
with respect to the actual performance of the graphics hardware (expressed as
frame rate). For instance anti-aliasing is automatically turned off when a molecular
scene is manipulated (rotated, translated, zoomed)<!--, though when no further mouse
events are encountered anti-aliasing is automatically turned on again-->.</p>


<h5><a class="anchor" name="fog"><B>Depth cue</b> menu item</a></h5>

<p>Depth cue is often referred to as the fog effect. When this option is selected
the molecular scene is drawn as if it was placed in a foggy atmosphere which
results in displaying distant parts of the molecules with faded, blurred colors while
near parts are brighter with sharper edges. This gives a good impression of depth
that allows better recognize the 3D structure.</p>


<h5><a class="anchor" name="antialias"><B>Anti-alias</b> menu item</a></h5>

<p>Anti-aliasing smooths all objects displayed that results in smoother edges,
less ragged lines, more realistic intersections. However, this function
is very costly and the quality highly depends on the graphic hardware.<br>
Note, that anti-aliased scene cannot be manipulated (rotated, zoomed etc)
therefore a built in mechanism called quality auto scaling, unique to MarvinSpace,
automatically turns off anti-aliasing for moving images and turned it back when
image is standing still.</p>


<h5><a class="anchor" name="options"><B>Options</b> menu item</a></h5>

<p>This menu item pops up a dialog window to set various rendering parameters.
These are as follows.</p>

<B>Visualizers</b> tab that applies to Ligands, MacroMolecules, Water and Ions:

<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Parameter</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Ball radius</b></td>
            <td>Size of atom spheres in <B>Ball</b>
                draw type, measured in Angstroms.</td>
        </tr>
        <TR>
            <TD><B>Bond radius</b></td>
            <td>Size of bond cylinders in <B>Ball and Stick</b>
                draw type, measured in Angstroms.</td>
        </tr>
        <TR>
            <TD><B>Stick radius</b></td>
            <td>Size of bond cylinders in <B>Stick</b>
                draw type, measured in Angstroms.</td>
        </tr>
        <TR>
            <TD><B>Line width</b></td>
            <td>Width of bonds in wire mode.</td>
        </tr>
        <TR>
            <TD><B>Double bond distance</b></td>
            <td>Gap between two lines/sticks representing a double bond. It is
                determined as a percentage of Bond radius.</td>
        </tr>
        <TR>
            <TD><B>Double bond width</b></td>
            <td>Thickness of line/stick representing a double bond. It is
                expressed relative to the thickness of a single bond.</td>
        </tr>
        <TR>
            <TD><B>Display bond order</b></td>
            <td>When checked double bonds are drawn by two line segments,
                otherwise all bonds are represented as single bonds. <br>
                Future releases will introduce drawing mode for triple and aromatic
                bonds too.
                </td>

        </tr>
        <TR>
            <TD><B>vdW scaled balls</b></td>
            <td>When checked atom spheres in Ball and Ball-and-Stick modes are scaled according to
                their van der Waals radii. Otherwise all atoms (apart from hydrogen) are represented by
                uniform sphere radii. Hydrogen radius is half of atom radius.
            </td>
        </tr>
        <TR>
            <TD><B>Smooth colored sticks</b></td>
            <td>When checked bi-colored stick bonds are
                colored gradually from one color to the other (in CPK atom
                coloring mode). Otherwise the two halves are draw with the two
                different colors.
            </td>
        </tr>
    </table>
</center>

<br>
<B>Surface</b> tab:
<br>

<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Parameter</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Probe radius</b></td>
            <td>Radius of probe atom representing solvent when constructing
                the Connolly and the solvent accessible surfaces. Measured in Angstroms.</td>
        </tr>
        <TR>
            <!--<TD><B>Grid resolution</b></td>
            <td>Size of grid cells in surface calculations, measured in
                Angstroms. The smaller the value, the finer the surface and the
                longer the surface calculation takes. Also, finer resolution
                grids require significantly more working memory.</td>-->
            <TD><B>Automatic surface resolution</b></td>
            <td>Size of grid cells in surface calculations will be set automatically
            according to the number of atoms.</td>
        </tr>

        <TR>
            <TD><B>Manual surface resolution</b></td>
            <td>Size of grid cells in surface calculations can be given, measured in
                Angstroms. The smaller the value, the finer the surface and the
                longer the surface calculation takes. Also, finer resolution
                grids require significantly more working memory.</td>
        </tr>
        <TR>
            <TD><B>Surface triangle count reduction</b></td>
            <td>When checked, the number triangles constituting a molecular
                surface are reduced without effecting the smoothness of the
                surface. This step is performed after the surface is calculated
                and it takes some time particularly for larger surfaces. However, it
                is worth spending some extra time for triangle reduction because
                the resulting surface can be displayed and manipulated much
                faster than the original surface.</td>
        </tr>
    </table>
</center>
<br>
<b>Secondary Structure tab:</b>

<p>Various settings of the secondary structure representation.</p>

<B>Colors</b> tab:

<p>Change default colors here. Note, that in MarvinSpace 1.3 chain colors
are wired in and cannot be changed by the user.<br>
The following colors can be changed:</P>
<ul>
    <li>Constant color of components: Ligand, MacroMolecule, Water, Ion, Surface</li>
    <li>Constant color of secondary structure: Helix, Sheet, Turn, Coil</li>
    <li>CPK Color of the following atoms: H, C, N, O, S, P and Unknown atoms</li>
    <li>Color of selections</li>
    <li>Background color, this can also be set to transparent or to smooth colored (shaded).</li>
    <li>Residue color schema can be changed to the one defined in SETOR <br>
        (written by Stephen Evans,
        <i>SETOR: hardware-lighted three-dimensional solid model representations of macromolecules.
        J Mol Graph. 1993, 11, 134-138.)</i></li>
</ul>


<p>
<a class="text" name="controlstab"><B>Controls</b> tab:</a></P>

<p>This allows the user to customize how MarvinSpace reacts to various input
events (like mouse motion, clicking etc). Note, that not all, but most of the
important actions can be customized.</P>


<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Parameter</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Default style</b></td>
            <td>With this user can select MarvinSpace style association
                of input <a href="#eventsandactions">events with actions</a>.</td>
        </tr>
        <TR>
            <TD><a class="text" name="customstyle"><B>Custom style</b></a></td>
            <td>User can select which mouse event will perform rotation, zooming, translation
                and will pop up the menu.</td>
        </tr>
        <TR>
            <TD><B>Invert zoom</b></td>
            <td>Swaps between zooming policies. By default zoom in is associated
                to moving mouse away from us (thus towards the scene), while
                zooming out is done in the opposite direction. However, when
                this option box is checked the zooming directions swap.</td>
        </tr>
        <TR>
            <TD><B>Animated rotation</b></td>
            <td>When checked, rotation will not stop when mouse movement stops
                but continues for a while depending on the acceleration/deceleration of
                the mouse while it was moving. This results in an inertia effect.
                Useless, but nice!</td>
        </tr>
    </table>
</center>


<B>Others</b> tab:

<p>Managing license keys.</p>

<h4><a class="anchor" name="showmenu">Show menu</a></h4>
<h5><a class="anchor" name="labelmenu"><b>Label</b> submenu</a></h5>
<p>In MarvinSpace any visible element can be labeled. Though from the gui only named
components can be labeled such as atoms, residues, molecules and secondary structures.
The labels can be colored to enhance visibility.</p>

<p><B>Labels on selection</b> is an other way of displaying labels on a visible element by selection.
In case of selecting atoms, if this box is checked the residue atom
label of the selected atoms are displayed next to the atom. The residue atom
label consists of the residue name (3 letter abbreviation in the case of amino
acids, or 1 letter code in the case of nucleic acids), the residue sequence number,
the chain identifier and the atom label.<br>
</p>


<h5><a class="anchor" name="surfacemenu"><B>Surface</b> submenu</a></h5>

<p>There are four types of molecular surfaces available in MarvinSpace: Connolly,
van der Waals, solvent accessible and blobby. Blobby molecule is yet experimental.</p>

<p><B>
Secondary structure</b> represents the secondary structure of protein components
by a schematic diagram.</p>

<h4><a class="anchor" name="animationmenu">Animation menu</a></h4>
<p>A simple built-in animation can be played by the <b>Play Demo</b> menu. Continous rotation is also
available by selecting <b>Idle Rotation</b>.</p>

<h4><a class="anchor" name="layoutmenu">Layout menu</a></h4>

<p>The MarvinSpace canvas can be subdivided into rectangular areas called cells.
Each cell can contain arbitrary number of structures. Each cell is fully
functional, that is, the same actions can be performed per cell as for an
undivided canvas.</p>

<CENTER>
    <TABLE WIDTH="90%" BORDER=0 CELLPADDING=5 cellspacing="0" class="grid">
        <tr><Th width="30%"><B>Parameter</b></Th><th WIDTH="70%">Description</th></TR>
        <TR>
            <TD><B>Add row</b></td>
            <td>Inserts a new row of cells below the last row. The new row
                contains as many cells as many columns are displayed.</td>
        </tr>
        <TR>
            <TD><B>Add column</b></td>
            <td>Inserts a new column of cells after the last column. The new
                column contains as many cells as many rows are already
                displayed.</td>
        </tr>
        <TR>
            <TD><B>Delete row</b></td>
            <td>Removes the last (bottom) row (that is, all cells in the last
                row) and the content of cells.</td>
        </tr>
        <TR>
            <TD><B>Delete column</b></td>
            <td>Removes the last (right hand site) column along with all of
                its cells and the content of cells.</td>
        </tr>
        <TR>
            <TD><B>Reset view in all cells</b></td>
            <td>Reverts view angle and zoom position in all cells.</td>
        </tr>
        <TR>
            <TD><B>Synchronous mode</b></td>
            <td>When checked, all motion events are delivered to all cells.
                This means that rotating the content of the cell under the mouse
                pointer affects all other cells as if the mouse was moved the
                same way in those cells too.</td>
        </tr>
    </table>
</center>


<h3><A class="anchor" NAME="popupmenu">Popup Menu</A></h3>

<P>The Popup menu appears when you <a href="#customstyle">right-click</a> over
the canvas. Functions available in this menu will significantly change in
future releases.<br>
In version 1.3 the Popup menu looks like as on the image.
<img src="space-gui_files/popup.png" align=RIGHT alt="Popup Menu">
</P>
<ul>
    <li>The first item, <B>Best fit</b>, works well in all cases. This sets zoom ratio
and view angle to optimal values to allow to see the entire content of the current cell (where
right mouse button was pressed) regardless of the size and the number of structures displayed
in that cell.</li>
    <li><a href="space.html#zoomtopocket"><b>Zoom to pocket</b></a> is a combination
    of selections and hide events offering a quick way of restraining the view to a binding pocket.</li>
    <li>Atom selections can be extended to whole residues by the next menu.</li>
    <li><b>Show</b> and <b>Show monitors</b> do not change the viewing transformations,
    just set invisible components to be ideally visible. To have a component being visible in fact,
    it may also be necessary to use Best fit.</li>
    <li>The <b>Hide</b> menu items can be used on graphic components and on parts of components,
    for example atoms.</li>
    <li><b>Fade</b> is similar to Hide in the sense that it helps reducing the view to
    the interesting part. Faded components are usually drawn with dark gray color,
    they are not considered during Best fit, and they cannot be picked by the mouse.
    So the behaviour of hidden and faded elements is the same,
    the difference is that faded elements can be seen.</li>
    <li><b>Delete</b> is the way of removing components finally from the scene.
    There is a great difference between deleting and the upper operations as Show, Hide and Fade:
    Delete is defined only on complete components, so for example atoms cannot be deleted.</li>
</ul>


<h3><a class="anchor" name="toolbar">Toolbar</a></h3>

<p>The Toolbar is located under the Main menu bar and it consists of small
icon buttons. These allow to access functions not available in menus. (Note,
that future releases of MarvinSpace will make all functions available from
dedicated submenus too, and the Toolbar will be user configurable.)<br>
There are various classes of functions available as tools, such as monitors, controls,
pharmacophores and other display tools.</p>


<h4><a class="anchor" name="monitors">Monitors</a></h4>

<p>These tools enable to measure  geometric properties of molecules in
an interactive fashion. Distances (bond lengths or any interatomic distances),
bond angles and dihedral angles can be measured. Results are displayed in
monitors that are small labels on the canvas linked to the structure. When the
structure is rotated these monitors move along, and when the structures are
manipulated by <a href="#controls">controls</a> monitors are refreshed
automatically to reflect any changes in the geometry of the structures instantly.</p>

<p>Monitors are easy to use: select the type of monitor appropriate for the
property to be measured (ie. distance, bond angle, dihedral angle), then
select the appropriate number of atoms one by one (single click with left mouse
button). When the last atom (ie. second, third or fourth depending on the
type of monitor) is selected the monitor appears on the canvas.</P>

<img src="space-gui_files/monitors.png" align=MIDDLE alt="Monitors in MarvinSpace"/>

<p>Monitors themselves can be selected by single click of left mouse button just like any
other component visible on the canvas. When selected, they can be deleted (ie.
removed forever), and they can also be hidden (ie. removed from the canvas
temporarily). Hidden monitors can be shown again, use the right mouse button
<a href="#popupmenu">popup menu</a>.</p>


<h4><a class="anchor" name="controls">Controls</a></h4>

<p>Controls are tools that can manipulate the internal and absolute coordinates or other
geometrical properties of the selected objects. Three controls are available:
translate, rotate and resize. The latter, resize, can be applied to
elements of <a href="#pharmacophore">pharmacophore models</a> or to surfaces.<p>

<img src="space-gui_files/controls.png" align=MIDDLE alt="Controls in MarvinSpace"/>

<p>The translate control moves the selected object and changes its coordinates, thus the
relative position of two (or more) objects (e.g.. two ligands in the same
binding pocket) can be modified. To translate a molecule follow the steps below:</p>

<ol>
    <li>Select the structure in the <a href="#selectionPanel">selection panel</a>: click on it with the left mouse button</li>
    <li>click right button to get the popup menu</li>
    <li>choose first item, <B>Select</b>, atoms of the
        selected structure become highlighted</li>
    <li>now press the translate control button in the Toolbar: <img src="space-gui_files/translate.png" alt="icon"/></li>
    <li>drag the selected object: hold down the left mouse button plus press
        the <B>Ctrl</b> (control) key on the keyboard and
        move the mouse</li>
</ol>

<p>Note, however, that this way the selected object can be translated in the
plane of the screen only. In order to move it in other directions, that is, along
the third axis towards the viewer's eyes or away from them, the <B>Shift</b>
key has to be pressed too. <br>
Note that rotation and translation of the scene is always possible, regardless of
which monitor or control is being applied.</p>

<p>The next control button is the rotation control. With this the selected
structure can be rotated without affecting any other object. For instance a ligand in a proteins binding
pocket can be rotated while the protein
remains in its original position. To rotate the selected object follow the steps
of translation described above, except that in the 4th step press the rotate
control button instead of the translate button: <img src="space-gui_files/rotate.png" alt="icon"/>
<br>Note, that the <B>Ctrl</b> (control) key on the keyboard has to be held down to
rotate the selected object, otherwise the scene is rotated (thus no coordinates,
relative positions of objects changes).<br>
If both <B>Ctrl</b> (control) and
<B>Shift</b> keys are pressed, the object rotates about
the axis perpendicular to the plane of the canvas.
</P>

<p>The resize control can be applied to increase/decrease the size of spheres
and arrows used in <a href="#pharmacophore">pharmacophore model building</a>.
<img src="space-gui_files/resize.png" alt="icon"/>
<br>This works similar to translation and rotation, though in this case the
object to be selected is either a pharmacophore sphere or an arrow. Again, the
<B>Ctrl</b> (control) key has to pressed to resize the
selected object.
Resize also has effect on surfaces. In this case the bounding box of a selected surface
can be resized, and thus the surface will be clipped by 6 clipping planes determined
by the sides of the bounding box.</p>

<h4><a class="anchor" name="pharmacophore">Pharmacophore model building</a></h4>

<p>MarvinSpace offers a simple tool to represent pharmacophore models: spheres
and arrows can be placed at any position. These can be translated, rotated and
resized using controls.</p>

<img src="space-gui_files/phmb.png" align=MIDDLE alt="Pharmacophore types in MarvinSpace"/>

<p>To place a pharmacophore sphere to represents a pharmacophore point
follow the steps below:</p>

<ol>
    <li>press the pharmacophore sphere button</li>
    <li>click on an arbitrary atom: a sphere appears around the
        selected atom</li>
</ol>

<p>Arrows can be placed the same way except that the arrow button has to be
pressed to initiate the process. </p>


<h4><a class="anchor" name="displaytools">Display tools</a></h4>

<p>Display tools enhance the visualization capabilities of MarvinSpace. With these
the user can have better understanding of the structures studied.<br>
The <B>Depth cue</b> (or Fog) tool enhances the sensation
of space (depth) by fading distant objects. The fog can gradually be adjusted
by the <B>Depth cue</b> slider.</p>
<img src="space-gui_files/fog.png" align=MIDDLE alt="Depth cue slider image"/>

<p>The <B>Clipping</b> slider is a composite slider. It moves two planes parallel with the
canvas towards or away from the visible objects. One of the planes (the near plane) cuts
these object so that parts in front of the plane will not be visible. The other plane (the far plane)
cuts parts that are behind the plane. This helps better understand the
structure being analyzed by allowing deeper insight into buried parts by hiding
obscuring details.</p>
<img src="space-gui_files/clipping.png" align=MIDDLE alt="Clipping slider image"/>

<p>The <b>Isosurface</b> slider is yet an experimental slider. Its aim is to easily
change the threshold value of isosurfaces. Isosurfaces in MarvinSpace 1.3 appear only
when Gaussian Cube files are imported. In this case an isosurface is automatically
generated, and it can be changed interactively (depends on the size of the volume
and the computer capacity) by changing the threshold value with the slider.</p>
<img src="space-gui_files/isosurface.png" align=MIDDLE alt="Isosurface image"/>

<p>Finally, the tool for <a class="text" name="dynamicsurfacecolor"><b>dynamic surface coloring</b></a>
is more complex. In the present
release it can be used in combination with surfaces colored by electrostatic
potential.<br>
By moving the sliders the areas of the surface where the negative/positive
potential is below/above the threshold values set by the slider are not colored
(i.e.. colored by the default color).<br>
The leftmost and rightmost edit boxes display the minimum/maximum potential
values calculated on the surface, while the two inner values correspond to
the actual positions of the slider in the [minimum, 0] and the [0, maximum] ranges, respectively.<br>
By clicking on the colored image above the sliders, the palette can be changed
by selecting a palette from a list on an appearing dialog.<br>
With this dynamic coloring modelers can better focus on areas where the
absolute value of the potential is above a certain threshold thus where
the chance for an electrostatic interaction is more likely.
</p>
<img src="space-gui_files/color.png" align=MIDDLE alt="Color slider image"/>


<h3><A class="anchor" NAME="selectionPanel">Selection panel</A></h3>

<p>Components in MarvinSpace are registered in the selection panel in hierarchical way.
Macromolecules may consist of Chains, Ligands, Ions and Water. Computed molecular surfaces
and the secondary structure are also displayed under the related macromolecule.<br>
Components being in an inactive cell will appear faded and selecting them will cause the
activation of the containing cell.<br>
Every component has a symbolic image on the selection panel that is a rectangle
with a specific color. The color helps identifying the structures.
For example when macromolecule chains are colored by chain type the related symbolic images will
have the same color as the chain. By clicking on a symbolic image a component can
be shown/hidden quickly and the image changes the visibility state of the components.
</p>

<table>
    <tr>
        <td><img src="space-gui_files/selectionpanel.png" align=MIDDLE alt="Selection panel of MarvinSpace"/></td>
        <td><img src="space-gui_files/pdbinfo2.png" align=MIDDLE alt="PDB Information"/></td>
    </tr>
</table>

<p>The selection panel has its own <b>Popup Menu</b> that contains submenus and menu
items according to the selected component. Components can be selected/deselected,
shown/hidden, closed and have their display properties changed independently.
There are some actions that are not available from the <a href="#menubar">Menubar</a>,
because they are connected to specific components.</p>

These are as follows:<br>
<p><b>Information</b> of MacroMolecules displays variuos information found in pdb files.</p>
<p><b>Selecting the neighborhood of a ligand</b> causes the selection of all components or
    parts of components (atoms) lying in a customizable size environment of the specified ligand.
    This is useful when dealing with large macromolecules because the display can be
    greatly reduced to the interesting part of the molecule by choosing
    <b>Hide unselected components</b> in the main Popup menu.</p>
<p><b>Extending selection</b> of a chain will cause the selection of every atoms of every residue
    that have at least one atom already selected. Hidden atoms will also be selected
    and become visible.</p>
<p><b>Reduce triangle count</b> will take effect on a specific surface. Each time this is
    invoked the number of triangles will be reduced. Note, that invoking it many times will
    totally deform the surface.</p>
<p><b>Significant drawing</b> of a surface is used when the surface is colored by
electrostatic potential. In this case surface triangles where the potential is
between the two threshold value will not be drawn.</p>

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